Package Details: picard-tools 2.20.1-1

Git Clone URL: https://aur.archlinux.org/picard-tools.git (read-only, click to copy)
Package Base: picard-tools
Description: set of tools for working with next generation sequencing data in the BAM format
Upstream URL: https://github.com/broadinstitute/picard
Licenses: GPL2
Submitter: mschu
Maintainer: greyltc
Last Packager: greyltc
Votes: 7
Popularity: 0.000070
First Submitted: 2013-11-25 11:23
Last Updated: 2019-05-25 20:30

Latest Comments

« First ‹ Previous 1 2

greyltc commented on 2015-03-17 11:46

@wookietreiber, could you please add the following two lines to package():

mkdir -p $pkgdir/etc/profile.d
echo 'export PICARDROOT="/usr/share/java/picard-tools"' > $pkgdir/etc/profile.d/picard-tools.sh

thanks!

greyltc commented on 2015-01-15 23:36

python should be added to the build time dependencies:
...
- Building main bedtools binary.
done.
- Creating executables for old CLI.
/bin/bash: python: command not found
make: *** [all] Error 127
Makefile:99: recipe for target 'all' failed
==> ERROR: A failure occurred in build().
Aborting...
==> ERROR: Makepkg was unable to build bedtools.
...

wookietreiber commented on 2014-11-20 10:38

1.125 just got released [1], see PKGBUILD [2].

[1]: https://github.com/broadinstitute/picard/releases/tag/1.125
[2]: https://github.com/wookietreiber/PKGBUILDs/tree/master/picard-tools

MikeDacre commented on 2014-11-19 18:32

Thanks for the PKGBUILD wookietreiber, applied. Apologies for the delay, I was away.

alexpe87 commented on 2014-11-19 11:09

MikeDacre doesn't seem to be happy to update this to something more current...though the PKGBUILD from wookietreiber works perfectly fine.

wookietreiber commented on 2014-11-13 12:49

Update: I just renamed the bin file to just picard:

$ picard -h
$ picard SortSam -h

wookietreiber commented on 2014-11-13 12:18

Upstream devs changed the way separate tools are deployed: now there is only a single jar which contains all the command line tools, see release notes [1].

See [2] for an updated PKGBUILD. This provides a single 'picard-tools' in /usr/bin. With this you can access all the tools:

$ picard-tools -h
$ picard-tools SortSam -h

[1]: https://github.com/broadinstitute/picard/releases/download/1.124/README.txt
[2]: https://github.com/wookietreiber/PKGBUILDs/tree/master/picard-tools

alexpe87 commented on 2014-09-06 12:00

There seems to be a bug inside this package:

AddOrReplaceReadGroups calls CreateSequenceDictionary unfortunately....so the links seem to be wrong...